rs2143417

Variant names:

• chr1-186684655-G-T
• rs2143417

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.218 in 152,048 control chromosomes in the GnomAD database, including 4,658 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.22 (4658 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33101 AN: 151930 Hom.: 4638 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.0493

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.0866

Gnomad MID AF: 0.224

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.221

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.218 AC: 33160 AN: 152048 Hom.: 4658 Cov.: 32 AF XY: 0.213 AC XY: 15820 AN XY: 74346

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.0491

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.0866

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.224

Alfa AF: 0.174 Hom.: 1236

Bravo AF: 0.234

Asia WGS AF: 0.159 AC: 555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.62

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2143417; hg19: chr1-186653787;